Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2, Colombia.

Coronavirus disease (COVID-19) in Colombia was first diagnosed in a traveler arriving from Italy on February 26, 2020. However, limited data are available on the origins and number of introductions of COVID-19 into the country. We sequenced the causative agent of COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), from 43 clinical samples we collected, along with another 79 genome sequences available from Colombia. We investigated the emergence and importation routes for SARS-CoV-2 into Colombia by using epidemiologic, historical air travel, and phylogenetic observations. Our study provides evidence of multiple introductions, mostly from Europe, and documents >12 lineages. Phylogenetic findings validate the lineage diversity, support multiple importation events, and demonstrate the evolutionary relationship of epidemiologically linked transmission chains. Our results reconstruct the early evolutionary history of SARS-CoV-2 in Colombia and highlight the advantages of genome sequencing to complement COVID-19 outbreak investigations.

Risk factors associated with Chagas disease in pregnant women in Santander, a highly endemic Colombian area.

OBJECTIVE: To determine the prevalence and risk factors associated with Chagas disease in pregnant women in an endemic area of Santander, Colombia. METHODS: Cross-sectional study included 23 municipalities of Santander, Colombia. Serological IFAT and ELISA tests were undertaken to detect IgG anti- Trypanosoma cruzi. A questionnaire was conducted for assessing the risk factors of each participant. Newborns were evaluated at birth and followed up to 1 year of age to determine congenital infection. RESULTS: An overall prevalence of 3.2% (95% CI 2.4-4.2) among 1518 pregnant women was detected. Prevalences by provinces were as follows: Guanentina: 6.0% (95% CI 4.1-8.5), García Rovira: 2.9% (95% CI: 1.5-4.8) and Comunera: 0.4% (0.4-2.3). The main risk factors identified were age >32 years old (OR: 2.1; 95% CI: 1.1-3.9); currently having a thatched roof (OR: 11.8; CI95% 2.2-63.2) and a thatched roof during childhood (OR: 3.0; 95% CI: 1.4-6.6); having below primary school education level (OR: 4.6; 95% CI: 2.2-9.5); and a history of a close contact with the vector (triatomine bugs) at least once during their lifetime (OR: 6.9; 95% CI: 3.7-12.9). No congenital cases were detected by parasitological or serological techniques. CONCLUSIONS: Prevalence of Chagas disease in pregnant women is a potential source of infection in this Colombian endemic area. The main risk factors associated with seropositivity were related to conditions favouring the contact with the vector. The results show that it is necessary to continue an active surveillance in order to offer diagnosis and treatment to mothers and their newborns in addition to screening to pregnant women from endemic areas.

Prevalence and risk factors for Chagas disease in pregnant women in Casanare, Colombia.

Knowledge of the prevalence and risk factors associated with maternal infection is the first step to develop a surveillance system for congenital transmission of Chagas disease. We conducted a cross-sectional study in Casanare, a disease-endemic area in Colombia. A total of 982 patients were enrolled in the study. A global prevalence of Trypanosoma cruzi infection of 4.0% (95% confidence interval [CI] = 2.8-5.3%) was found. Multivariate analysis showed that the most important risk-associated factors were age > 29 years (adjusted odds ratio [aOR] = 3.4, 95% CI = 0.9-12.4), rural residency (aOR = 2.2, 95% CI = 1.0-4.6), low education level (aOR = 10.2, 95% CI = 1.6-82.7), and previous knowledge of the vector (aOR = 2.2, 95% CI = 1.0-4.9). Relatives and siblings of infected mothers showed a prevalence of 9.3%. These findings may help physicians to investigate congenital cases, screen Chagas disease in siblings and relatives, and provide early treatment to prevent the chronic complications of Chagas disease.

Caracterización molecular de los genes histona H2A y ARNsno-Cl de Trypanosoma rangeli: aplicación en pruebas diagnósticas / Molecular characterization of histone H2A and snoRNA-Cl genes of Trypanosoma rangeli: application in diagnostic tests

La aplicación de la reacción en cadena de la polimerasa (PCR) para detectar e identificar Trypanosoma rangeli y Trypanosoma rangeli presenta a menudo dificultades de interpretación. Así, algunas pruebas generan la amplificación de bandas similares provenientes de uno de los dos parásitos, fragmentos polimórficos de un mismo parásito, o la prevalencia en la detección de T. cruzi en infecciones mixtas. En este estudio se presentan y analizan los trabajos de investigación básica realizados con el objeto de diseñar y estandarizar pruebas de PCR específicas de cada parásito. Los iniciadores TcH2AF/R se diseñaron sobre la base de la región diferencial observada entre las unidades génicas que contienen los genes h2a en estos tripanosomas. Esta pareja de iniciadores amplifican un fragmento de 234 pb específico para T. cruzi (cepas I y II). Los iniciadores TrF/R2 anillan en las regiones intergénicas del fragmento génico de 801 pb codificante para seis transcritos que forman la agrupación ARNsno-Cl en T. rangeli. Estos iniciadores amplifican un fragmento de 620 pb exclusivo de las cepas KP1(-) y KP1(+) de este parásito. La aplicación de estas PCR en vectores infectados y en pacientes con enfermedad de Chagas muestra que ambas pruebas constituyen herramientas útiles para el diagnóstico y la identificación diferencial de estos tripanosomátidos.

The application of polymerase chain reaction (PCR) to detect Trypanosoma rangeli and Trypanosoma rangeli often presents interpretation challenges. For example, some tests yield the amplification of similar bands from either parasite, polymorphic fragments of the same parasite, or present deviation towards T. cruzi in mixed infections. In this study, the basic researching needed for designing and standardizating specific PCR tests for each parasite species PCR are shown and analyzed. The TcH2AF/R primers were designed on the basis of the differential gene region observed between the histone h2a genic units of these parasites. These primers amplify a specific 234 bp fragment in T. cruzi (T. cruzi I and II strains). The TrF/R2 primers anneal to the intergenic regions of an 801 bp gene fragment encoding for six transcripts that conform the snoRNA-Cl cluster in T. rangeli. These primers amplify a fragment of 620 bp exclusively in KP1(-) and KP1(+) strains of the parasite. The application of these PCR tests in infected vectors and in chagasic patients show that both tests constitute useful tools for the diagnosis and differential identification of these Trypanosomatids. Key words: histone, RNA small nucleolar (snoRNA), polymerase chain reaction (PCR), Trypanosoma.

[Comparison of a PCR test based on the histone H2A/SIRE genes with classical serological tests for the diagnosis of chronic Chagas disease in Colombian patients]. / Comparación de una prueba de PCR basada en los genes codificantes para la histona H2A/SIRE con pruebas serológicas convencionales para el diagnóstico de la enfermedad de Chagas crónica en pacientes colombianos.

INTRODUCTION: Diagnosis of Chagas disease in its latent and chronic phase is difficult because of the low parasitemia levels. Therefore, serological and molecular techniques are necessary to achieve an appropriate diagnosis. OBJECTIVE: The polymerase chain reaction based on the amplification of the SIRE element inserted into H2A encoding genes was compared with classical serological tests for the diagnosis of Chagas disease in Colombian patients. MATERIALS AND METHODS: An agreement study was carried out by comparing the PCR with ELISA (enzyme linked immuno sorbent assay) and IFAT (indirect immunofluorescence) tests. In addition, the PCR sensitivity and specificity were determined. A sample of 156 individuals was tested with the H2A PCR primers after a Chagas disease classification based on clinical, epidemiological and serological data associated with each patient. In addition, 97 out of 156 samples were also compared with the S35/S36 PCR primers. RESULTS: Eighty-nine of 156 samples (57%) were positive by both IFAT and ELISA and 84 (53.8%) presented the expected 234 bp amplification fragment. The sensitivity of the TcH2AF/ R PCR was 88% (95% C.I.: 75%--95%) and its specificity 92.5% (95% C.I.: 87.7%--97.2%). The kappa index for concordance between serological tests and TcH2AF/R PCR was 0.8 (95% C.I.: 73%--86%), and between the TcH2AF/R and S35/S36 PCR primers was 0.9 (95% C.I.: 84%-96%). These indices indicated a "good" and "almost perfect" agreement, respectively. CONCLUSIONS: The TcH2AF/R PCR is a promising diagnostic tool for the detection of T. cruzi and is suggested as a tool complementary to the classical serological tests.

Comparación de una prueba de PCR basada en los genes codificantes para la histona H2A/SIRE con pruebas serológicas convencionales para el diagnóstico de la enfermedad de Chagas crónica en pacientes colombianos / Comparison of a PCR test based on the histone H2A/SIRE genes with classical serological tests for the diagnosis of chronic Chagas disease in Colombian patients

Introducción. El diagnóstico de la enfermedad de Chagas en sus fases latente y crónica se dificulta por la baja parasitemia, razón por la cual se recurre a métodos serológicos y moleculares. Objetivo. Comparar la prueba de reacción en cadena de la polimerasa basada en la amplificación del elemento SIRE insertado en el gen que codifica para la histona H2A con las pruebas serológicas convencionales para el diagnóstico de la enfermedad de Chagas en pacientes colombianos. Materiales y métodos. Se realizó un estudio de concordancia comparando la PCR TcH2AF/R con las pruebas de inmunoensayo enzimático e inmunofluorescencia indirecta, determinándose además la sensibilidad y especificidad de la prueba. Se clasificaron y examinaron 156 individuos según los hallazgos clínicos y epidemiológicos y los resultados de las pruebas serológicas. Adicionalmente, 97 de las 156 muestras fueron comparadas con la PCR S35/S36. Resultados. De 156 muestras, 89 (57 por ciento) fueron positivas por IFI y ELISA, y 84 (53,8 por ciento) presentaron el perfil de amplificación correspondiente a la banda esperada de 234 pb, obteniéndose una sensibilidad de 88 por ciento (I.C. 95 por ciento: 75 por ciento - 95 por ciento) y especificidad de 92,5 por ciento (I.C. 95 por ciento: 87,7 por ciento - 97,2 por ciento). El índice kappa, indicador de concordancia entre las pruebas serológicas y TcH2AF/R fue de 0,8 (I.C. 95 por ciento: 73 por ciento - 86 por ciento), en tanto entre las PCR TcH2AF/R y S35/S36 fue de 0,9 (I.C. 95 por ciento: 84 por ciento - 96 por ciento), interpretados como una concordancia buena y casi perfecta, respectivamente. Conclusiones. La PCR TcH2AF/R es una prueba diagnóstica promisoria complementaria a las pruebas serológicas, para la detección de Trypanosoma cruzi.

Introduction. Diagnosis of Chagas disease in its latent and chronic phase is difficult because of the low parasitemia levels. Therefore, serological and molecular techniques are necessary to achieve an appropriate diagnosis. Objective. The polymerase chain reaction based on the amplification of the SIRE element inserted into H2A encoding genes was compared with classical serological tests for the diagnosis of Chagas disease in Colombian patients. Materials and methods. An agreement study was carried out by comparing the PCR with ELISA (enzyme linked immuno sorbent assay) and IFAT (indirect immunofluorescence) tests. In addition, the PCR sensitivity and specificity were determined. A sample of 156 individuals was tested with the H2A PCR primers after a Chagas disease classification based on clinical, epidemiological and serological data associated with each patient. In addition, 97 out of 156 samples were also compared with the S35/S36 PCR primers. Results. Eighty-nine of 156 samples (57%) were positive by both IFAT and ELISA and 84 (53.8%) presented the expected 234 bp amplification fragment. The sensitivity of the TcH2AF/ R PCR was 88% (95% C.I.: 75%--95%) and its specificity 92.5% (95% C.I.: 87.7%--97.2%). The kappa index for concordance between serological tests and TcH2AF/R PCR was 0.8 (95% C.I.: 73%--86%), and between the TcH2AF/R and S35/S36 PCR primers was 0.9 (95% C.I.: 84%-- 96%). These indices indicated a “good” and “almost perfect” agreement, respectively. Conclusions. The TcH2AF/R PCR is a promising diagnostic tool for the detection of T. cruzi and is suggested as a tool complementary to the classical serological tests.